Extended Data Fig. 2: Cytokines secreted by CD4 T cells across transcriptional clusters.

a–d, Proportion of right colon lamina propria CD4 T cells expressing IL-17A (a), IFNγ (b), TNFα (c), or FOXP3 (d) after 3 hours of stimulation with PMA/ionomycin. e, Proportion of right colon lamina propria CD4 T cells that are IL-17A⁺ FOXP3^negative after 3 hours of stimulation with PMA/ionomycin. f, Proportion of right colon lamina propria CD4 T cells that are FOXP3⁺ IL-17A^negative after 3 hours of stimulation with PMA/ionomycin. g, h, Proportion of right colon lamina propria cells that are FOXP3^negative and IFNγ⁺ (g) or TNFα⁺ (h) after 3 hours of stimulation with PMA/ionomycin. i, j, Proportion of right colon lamina propria cells that are FOXP3⁺ and IFNγ⁺ (i) or TNFα⁺ (j) after 3 hours of stimulation with PMA/ionomycin. a–j, Significance determined by two-sided, unpaired Wilcox test without adjustment for multiple comparisons. A total of 6 PSC I2, 13 PSC I1, 18 PSC U, 3 IBD I2, 1 IBD I1, 12 IBD U, and 3 HC were included in the intracellular flow cytometry analysis. Not all samples were stained with every marker, resulting in a lower number than the total samples being included in the plots above. Center line represents the median value; hinges indicate the 1st and 3rd quartiles; upper and lower whiskers extend to the largest and smallest values that are within 1.5 times the interquartile range from 1st and 3rd quartiles, respectively.